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The trans-acting long noncoding RNA FLAIL represses flowering in Arabidopsis [ChIRP-seq]

ABSTRACT: The trans-acting long noncoding RNA FLAIL represses flowering in Arabidopsis [ChIRP-seq]

PROVIDER: PRJNA772980 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16497724_1.fastq.gz	Fastqsanger.gz
	SRR16497724_2.fastq.gz	Fastqsanger.gz
	SRR16497725_1.fastq.gz	Fastqsanger.gz
	SRR16497725_2.fastq.gz	Fastqsanger.gz
	SRR16497726_1.fastq.gz	Fastqsanger.gz

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The trans-acting long noncoding RNA FLAIL represses flowering in Arabidopsis [ChIRP-seq]

Project description:We identified differentially expressed genes in flail mutants linked to the regulation of flowering through stranded RNA-seq. A genomic rescue fragment of FLAIL (pFLAIL:gFLAIL) introduced in flail mutants can complement expression defects and early flowering, consistent with trans-acting effects of the FLAILRNA. We determined the genomic binding regions of FLAIL by ChIRP-seq. FLAIL binding to chromatin regions promotes the expression of selected flowering repressors.

2022-02-12 | GSE186214 | GEO

The trans-acting long noncoding RNA FLAIL represses flowering in Arabidopsis [RNA-seq]

2022-01-10 | GSE186212 | GEO

The trans-acting long noncoding RNA FLAIL represses flowering in Arabidopsis.

Project description:The trans-acting long noncoding RNA FLAIL represses flowering in Arabidopsis.

| PRJNA772961 | ENA

The trans-acting long noncoding RNA FLAIL represses flowering in Arabidopsis [RNA-seq]

Project description:The trans-acting long noncoding RNA FLAIL represses flowering in Arabidopsis [RNA-seq]

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Trans-acting regulatory variation in Saccharomyces cerevisiae

Project description:Natural genetic variation can cause significant differences in gene expression, but little is known about the polymorphisms that affect gene regulation. We analyzed regulatory variation in a cross between laboratory and wild strains of Saccharomyces cerevisiae. Clustering and linkage analysis defined groups of coregulated genes and the loci involved in their regulation. Most expression differences mapped to trans-acting loci. Positional cloning and functional assays showed that polymorphisms in GPA1 and AMN1 affect expression of genes involved in pheromone response and daughter cell separation, respectively. We also asked whether particular classes of genes were more likely to contain trans-regulatory polymorphisms. Notably, transcription factors showed no enrichment, and trans-regulatory variation seems to be broadly dispersed across classes of genes with different molecular functions

2010-06-05 | E-GEOD-617 | biostudies-arrayexpress

The trans-acting long noncoding RNA FLAIL represses flowering in Arabidopsis.

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-01-10 | GSE186215 | GEO

Trans-acting regulatory variation in Saccharomyces cerevisiae

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Somatic Primary piRNA Biogenesis Driven by Cis-Acting RNA Elements and Trans- Acting Yb

Project description:Primary piRNAs in Drosophila ovarian somatic cells arise from piRNA cluster transcripts and the 3′ UTRs of a subset of mRNAs, including Traffic jam (Tj) mRNA. However, it is unclear how these RNAs are determined as primary piRNA sources. Here, we identify a cis-acting 100-nt fragment in the Tj 3′ UTR that is sufficient for producing artificial piRNAs from unintegrated DNA. These artificial piRNAs were effective in endogenous gene transcriptional silencing. Yb, a core component of primary piRNA biogenesis center Yb bodies, directly bound the Tj-cis-element. Disruption of this interaction markedly reduced piRNA production. Thus, Yb is the trans-acting partner of the Tj-cis-element. Yb-CLIP revealed that Yb-binding correlated with somatic piRNA production but Tj-cis-element downstream sequences produced few artificial piRNAs. Thus, Yb determines primary piRNA sources by two modes of action; primary binding to cis-elements to specify substrates, and secondary binding to downstream regions to increase diversity in piRNA populations. HITS-CLIP of Yb in OSCs (Ovarian Somatic Cells) depleted for tj cis-element, and small RNA sequencing of Piwi-piRNAs in OSCs depleted for tj cis-element.

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The super-enhancer derived alncRNA-EC7/Bloodlinc potentiates red blood cell development in trans (ChIRP-seq)

Project description:Enhancer-derived RNAs are thought to contribute locally to their parent enhancers’ functions. Whether large domains of clustered enhancers (super-enhancers, SEs) also produce cis-acting RNAs, however, remains unclear. Unlike typical enhancers, SEs form large spans of robustly transcribed chromatin, amassing capped and polyadenylated RNAs that are sufficiently abundant to sustain trans functions. Here, we show that one such RNA, alncRNA-EC7/Bloodlinc, is transcribed from a SE of the erythroid membrane transporter SLC4A1/BAND3 but diffuses beyond this site. Bloodlinc localizes to trans-chromosomal loci encoding critical regulators/effectors of terminal erythropoiesis and directly binds chromatin-organizing and transcription factors, including the chromatin attachment factor HNRNPU. Inhibiting Bloodlinc or Hnrnpu compromises the terminal erythropoiesis gene program, blocking red cell production, whereas expressing Bloodlinc ectopically stimulates this program and can promote erythroblast proliferation and enucleation in the absence of differentiation stimuli. Thus, Bloodlinc represents a novel type of trans-acting SE RNA that potentiates red blood cell development.

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